Establishing farm dust as a useful viral metagenomic surveillance matrix

Kirsty T.T. Kwok; Myrna M.T. de Rooij; Aniek B. Messink; Inge M. Wouters; Lidwien A.M. Smit; Matthew Cotten; Dick J.J. Heederik; Marion P.G. Koopmans; My V.T. Phan

doi:10.1038/s41598-022-20701-x

Establishing farm dust as a useful viral metagenomic surveillance matrix

Kirsty T.T. Kwok^*, Myrna M.T. de Rooij, Aniek B. Messink, Inge M. Wouters, Lidwien A.M. Smit, Matthew Cotten, Dick J.J. Heederik, Marion P.G. Koopmans, My V.T. Phan^*

^*Corresponding author for this work

Virology

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85–100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.

Original language	English
Article number	16308
Journal	Scientific Reports
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41598-022-20701-x
Publication status	Published - 29 Sept 2022

Bibliographical note

Funding Information:
We thank all the participating farms for their cooperation, Pella van der Wal and Gaby van Dijk from Erasmus MC for providing sequencing service. This virome study was funded by ZonMW TOP project 91217040 (K.T.T.K., M.M.T.dR., L.A.M.S., D.J.J.H. and M.P.G.K.) and a Marie Sklodowska-Curie Individual Fellowship, supported by Horizon 2020 (grant no. 799417; M.V.T.P.). M.V.T.P and M.C. was additionally supported by the Wellcome Trust and FCDO (grant agreement number 220977/Z/20/Z, awarded to M.C.). Sample collection was supported with internal funds from the Utrecht University (M.M.T.dR., A.B.M., and I.M.W.).

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© 2022, The Author(s).

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title = "Establishing farm dust as a useful viral metagenomic surveillance matrix",

abstract = "Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85–100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.",

author = "Kwok, {Kirsty T.T.} and {de Rooij}, {Myrna M.T.} and Messink, {Aniek B.} and Wouters, {Inge M.} and Smit, {Lidwien A.M.} and Matthew Cotten and Heederik, {Dick J.J.} and Koopmans, {Marion P.G.} and Phan, {My V.T.}",

note = "Funding Information: We thank all the participating farms for their cooperation, Pella van der Wal and Gaby van Dijk from Erasmus MC for providing sequencing service. This virome study was funded by ZonMW TOP project 91217040 (K.T.T.K., M.M.T.dR., L.A.M.S., D.J.J.H. and M.P.G.K.) and a Marie Sklodowska-Curie Individual Fellowship, supported by Horizon 2020 (grant no. 799417; M.V.T.P.). M.V.T.P and M.C. was additionally supported by the Wellcome Trust and FCDO (grant agreement number 220977/Z/20/Z, awarded to M.C.). Sample collection was supported with internal funds from the Utrecht University (M.M.T.dR., A.B.M., and I.M.W.). Publisher Copyright: {\textcopyright} 2022, The Author(s).",

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AU - Smit, Lidwien A.M.

AU - Cotten, Matthew

AU - Heederik, Dick J.J.

AU - Koopmans, Marion P.G.

AU - Phan, My V.T.

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N2 - Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85–100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.

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Establishing farm dust as a useful viral metagenomic surveillance matrix

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